Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.

• Publication year

  2017

• Venue

  G3: Genes, Genomes, Genetics

• Publication date

  2017-03-31

• Fields of study

  Agricultural and Food Sciences, Medicine, Biology

• Identifiers
  DOI 10.1534/g3.117.041517PMID 28364039PMCID 5427501
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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• The Sequence Alignment/Map format and SAMtools

  2009influential reference
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  2009cited by this paper
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  2000influential reference
• Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv.

  1998cited by this paper
• Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa)

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• Microsatellite marker development, mapping and applications in rice genetics and breeding

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• Effects of genotype-environment interactions on genetic correlations

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  1987cited by this paper
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  1987cited by this paper
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  1980cited by this paper
• Rapid isolation of high molecular weight plant DNA.

  1980cited by this paper

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